Sunday, November 18, 2012

Michael Behe In Toronto: Part 1

Michael Behe was in Toronto last Thursday and Friday (Nov. 15 & 16, 2012). His visit was sponsored in part by the Copernicus Group, a group of Christian men who are interested in the dispute between science and religion. I met several of them (three physicians and an engineer).

The first of Behe's talks was organized by the Copernicus Group who invited faculty and graduate students from the Dept. of Biochemistry and the Dept. of Molecular Genetics to a session at Hart House in the afternoon. Only eleven people showed up—four (five?) of them were from the Copernicus group. There were ten bottles of wine!

This was the first time I had a chance to meet Michael Behe in person. He's a lot shorter than I imagined but otherwise looks just like his photos.

His talk was quite brief so we had a chance to ask questions and discuss his views. His main focus is on the existence of molecular machines and why that is evidence of design. He also emphasized the "limitations" of random mutation, claiming that they can't possibly supply the required variation needed in order for Darwinism to be a viable explanation of the history of life.

He's quite proud of his review in The Quarterly Review of Biology (Behe, 2012) where he tries to show that all of the mutations discovered in long-term evolution experiments are just examples of "loss-of-function" mutations that break an existing gene. There are many flaws with this perspective—see Jerry Coyne's review from Dec. 2010 [Behe’s new paper]. Naturally, Behe "forgot" to mention any of these objections.

I was very disappointed with the way Behe misrepresented evolutionary theory by talking only about Darwinism and natural selection. He did mention, in response to a question, that there were other "theories." The three he named were facilitated variation (Kirschner and Gerhart), Stuart Kauffman's ideas about self organization,1 and Lynn Margulis' views on symbiosis as a pervasive mechanism of evolution.

I asked him why he didn't talk about modern evolutionary theory that includes random genetic drift and the fixation of nearly neutral mutations. I mentioned that this isn't Darwinism by any stretch of the imagination—especially Behe's imagined definition of Darwinism—and that by incorporating modern evolutionary theory many of his arguments become moot. Behe replied that random genetic drift was not a mechanism of evolution because all it does shuffle existing mutations. Furthermore only "Darwinism" can account for the adaptive evolution that leads to improved life forms. (This is mostly true but Behe's main criticism is that evolution can't supply enough variation to do the job required of it and Neutral Theory accounts for all the observed variation that Behe ignores in his talks.)

One of the Copernicus Group physicians picked up on this and asked if there were any scientists who had another explanation for the evolution of complexity. Behe said "no." I pointed out that Michael Lynch and others have advanced perfectly reasonable non-adpative explanations of complexity. Behe asked me to repeat the name (Michael Lynch) then nodded knowingly. I asked if he had read Lynch's book (The Origin of Genome Architecture) and he said "yes." I don't understand why he doesn't discuss this in his lectures since it answers many of his "problems" with Darwinism.2

At that point my respect for Behe dropped considerably. Up until then I had been inclined to give him the benefit of the doubt and I had avoided calling him an IDiot. My respect soon dropped another notch when he said that he didn't accept endosymbiosis as the evolutionary explanation for the origin of mitochondria. Behe believes that evolution cannot explain how a primitive bacterium and a primitive eukaryotic cell could have co-adapted to form a cell with mitochondria. I think he means that mitochondria might have come from bacteria but that God had to tinker with the system quite a bit in order to come up with the required mutations for symbiosis.

The last straw for me was when Behe invoked the "Bozo the Clown" argument3 to justify the fact that modern evolutionary biologists reject Intelligent Design Creationism. This is one of the distinguishing characteristics of kooks. If you have to defend your views by pointing out that many great scientific ideas were initially rejected by the scientific community then you've already lost the battle. No legitimate scientist does this.

I'm afraid the Michael Behe is no better than Jonathan Wells, Casey Luskin, Bill Dembski, and the rest of the bunch at the Discovery Institute.

2. I'm being sarcastic. I know perfectly well why he doesn't mention it. It's because he doesn't know anything about Michael Lynch or nonadaptive evolution of complexity.

3. "But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown." Carl Sagan

Ah, so Behe is familiar with Lynch's work, but fails to mention it when asked about scientific explanations for the evolution of complexity. And you mention this, Bilbo, in Behe's DEFENSE? Maybe Behe would prefer you not defend him. Lying is a more serious offense than mere ignorance.

The comments by Behe do not refer specifically to Lynch's ideas about the evolution of nonadaptive complexity. Instead, Behe is responding to Lynch's criticism of an earlier Behe paper on the evolution of duplicated genes.

The crucial issue is that Behe wants all intermediates to be deleterious ...

Our model posited necessary intermediate mutations to be deleterious in the unduplicated gene; Lynch’s model assumes them to be neutral: “all 20 amino acids are equally substitutable in the intermediate neutral state” (Lynch 2005, this issue). All of his objections to our work stem from this difference.

This is a crucial difference. I went to three of Behe's talks while he was in Toronto and in all three talks he criticized the assumption that random mutation could generate complexity on the grounds that multiple mutations would have to occur simultaneously because each individual mutation would be harmful. He showed "adaptive landscapes" and pointed to the impossibility of getting off one peak in order to climb a higher one.

I think it would have been nice for Behe to mention that real scientists have other explanations.

And as he is a scientist doing enough work in the field to at least have the occasional publication, it's hard to believe he is not aware of those explanations. Which makes it difficult to avoid the conclusion that he is deliberately counting on his audience being actually unaware and therefore accepting his claims on faith. Not an unlikely scenario when there isn't someone like you (Larry) in the audience.

He is lying and he knows it. I'm tired of giving these people the benefit of the doubt, they've been given this for decades. There are no excuses any more, they're out to sell a worldview(and books) whatever it takes, even if they have to lie.

From the second mention of Lynch by Behe that I cite down below: http://behe.uncommondescent.com/2012/01/a-blind-man-carrying-a-legless-man-can-safely-cross-the-street/

"Finally, Thornton and colleagues latest work points to strong limits on the sort of neutral evolution that their own work envisions. The steps needed for the scenario proposed by Finnegan et al (2012) are few and simple: 1) a gene duplication; 2) a point mutation; 3) a second point mutation. No event is deleterious. Each event spreads in the population by neutral drift. Notice that the two point mutations do not have to happen together. They are independent, and can happen in either order. Nonetheless, this scenario is apparently exceedingly rare. It seems to have happened a total of one (that is, 1) time in the billion years since the divergence of fungi from other eukaryotes. It happened only once in the fungi, and a total of zero times in the other eukaryotic branches of life. If the scenario were in fact as easy to achieve in nature as it is to describe in writing, we should expect it to have happened many times independently in fungi and also to have happened in all other branches of eukaryotes.

It didn’t. Thus it seems a good conclusion that such neutral scenarios are much rarer than some workers have proposed (Gray et al, 2010; Lukes et al, 2011), and that more complex neutral scenarios are unlikely to happen in the history of life."

It sounds like Behe has less confidence in Lynch's theory than you do, Larry.

"It happened only once in the fungi, and a total of zero times in the other eukaryotic branches of life"

And what are Behe's references for this, Bilbo?

"It sounds like Behe has less confidence in Lynch's theory than you do, Larry."

Unfortunately, nowadays it's quite easy to point-mutate any gene we want to make changes to check protein structure and we know for sure that about 75-80% of mutations to a gene have no real effect on protein functionality. This is a fact, not a "theory", Bilbo. It's your own ignorance and desire for a creator that leads you to accept any piece of crap that Behe takes out of his ass as gospel. Behe gets it all wrong the moment that he assumes, with no evidence and against the facts, that most mutations are deleterious. Can you find ANY single modern paper on genetics that states this and wasn't written by an IDiot in their books or "scientific journals"?

Coyne and Lynch have done an excellent job of deconstructung Behe's argument and showing the fatal assumptions. They've made it clear that modern evolutionary theory is not Darwinism. Most of us have learned a thing or two about evolution since 1859. Behe refuses to acknowledge that science has moved on. He misrepresents evolution to his audiences.

True, but since Larry is suggesting that Behe is evading Coyne and Lynch's criticisms, I think it's important to note that he has indeed responded to them, which is information that Larry would never be willing to volunteer on his own.

I'm just a layman, so I wouldn't know if you are right or wrong. But a fair critc of Behe would at least point out that Behe has tried to respond to Lynch and Coyne. I do not believe Larry is being a fair critic.

Yes, NS is an important part of modern evolutionary theory. But modern evolutionary theory also recognizes that evolution is not just about NS. Unfortunately, this point doesn't always comes clear when you look at how basic Evolution courses present the issue. Students really need to dig deeper, because textbooks in general present a view of evolution that is to sanitized. I understand that you need to start with the basic premises since they are a good of teaching the basic concepts, but on the long run it's counterproductive.

Origin of Life/Chemical Evolution theories are far less reliable. We have good ideas, but there are so many possibilities and so little for now to go for that much of it is just informed hyphothesis more than what we expect from formal, robust theories. And yes, there's a lot of division there. Some people prefer the Metabolism First hyphotesis while other prefer the Methabolism Later. Some people prefer organic soups, others prefer hydrothermal vents, and still others prefer ice. Others see the RNA world as a strong case, others don't think it's reliable. And so on. We have good general arguments for some of these, informed by what we know of chemistry, but everything is still very fuzzy.

Evolution fundamentally arises out of sampling. A sample of any collection will almost certainly give a distorted representation of proportions of characters in the larger collection, and since offspring numbers vary (including zero), each generation is a distorted sample of the previous. This distortive effect compounds down the generations until one variant is fixed and the rest extinct.This is the baseline process: neutral drift.

Natural Selection is sample bias - a consistent effect for or against a variant due to a causal relationship with survival or reproduction of bearers. Turn up the intensity of selection and the contribution of drift diminishes, but the two are not a binary either/or.

So yes, NS is still part of evolutionary theory, but it is a component of a wider stochastic process: iterative population sampling. It's the bit that 'tunes' a population to its environment, so it's hardly inconsequential, but Drift has a big influence on variation and evolutionary 'exploration'.

Since both selection and drift require variants to do any work on population frequencies, this statement

Behe replied that random genetic drift was not a mechanism of evolution because all it does shuffle existing mutations

is particularly baffling. That's what all of evolution, apart from mutation itself, does.

"Let’s be clear: The work of science has nothing whatever to do with consensus. Consensus is the business of politics. Science, on the contrary, requires only one investigator who happens to be right, which means that he or she has results that are verifiable by reference to the real world. In science consensus is irrelevant. What is relevant is reproducible results. The greatest scientists in history are great precisely because they broke with the consensus.There is no such thing as consensus science. If it’s consensus, it isn’t science. If it’s science, it isn’t consensus. Period." . (From a lecture delivered by the late Michael Crichton at the California Institute of Technology)http://online.wsj.com/article/SB122603134258207975.html?mod=djemEditorialPage

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit')http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

"Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved."- Dr Behe in 1997

Genetic analysis of coordinate flagellar and type III - Scott Minnich and Stephen MeyerExcerpt: Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system.http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=389

I love Michael Cricton's books. He was a science fiction writer, not a scientist, nor a philosopher of science, nor a historian of science, or anything like that. His analysis in your statement is utterly wrong, consensus has an extremely important role in science, no scientist operates in a vacuum.

From footnote 2: "I'm being sarcastic. I know perfectly well why he doesn't mention it. It's because he doesn't know anything about Michael Lynch or nonadaptive evolution of complexity. "

Larry, you can claim that Behe "forgot" to mention Coyne's review, but did YOU not forget to mention that Behe actually responded to Coyne and Lynch specifically? That's a fact, whether Behe is right or wrong. Instead, you leave this information out and tell your readers that Behe doesn't know ANYTHING about them.

Please explain to me how your tactics are not dishonest. It seems pretty clear that your statements are ignorant at best. Care to defend yourself?

Laurence,That would be slightly better, since stating that Behe knows nothing about him is a factual mistake. Here are some points from one post Behe has made regarding Lynch:

Experimental studies contradict Lynch’s assumption of complete neutrality as a rule; the majority of amino acid substitutions decrease protein function.Lynch’s and our models are not mutually exclusive. Some evolutionary pathways might involve both deleterious and neutral mutations.Lynch writes in the section “The Model” that we “imply that all amino acid changes lead to nonfunctionalization.” We imply no such thing. Although we assumed that intermediate mutations required for a new feature decreased function, we wrote, “it can be calculated that on average a given position will tolerate about six amino acid residues and still maintain function.” Our estimation of ρ explicitly takes into account the tolerance of sites for substitution.In “The Model,” Lynch writes, “As in Behe and Snoke (2004), this adaptation is assumed to be acquired at the expense of an essential function of the ancestral protein. . . .” We made no such assumption. In our model, the final mutation might restore and enhance the original function.In the Discussion, Lynch writes, “It is difficult to pinpoint the source of the difference between the results of Behe and Snoke and those contained herein. . . .” The differences are largely due to opposing starting presumptions about whether mutations are deleterious.In the Discussion, Lynch writes, “Behe and Snoke assume that the forward and backward point-mutation rates (per amino acid residue) are equal.” We do not. The mutation rate we use is the nucleotide point-mutation rate.In the Discussion, Lynch writes that we assume mutations have “lethal pleiotropic effects.” We did not assume mutations to be either lethal or pleiotropic. We only assumed that they are “strongly selected against.”In the Discussion, Lynch writes, “If the intermediate steps . . . are entirely neutral after gene duplication, as Behe and Snoke assume, then there is no compelling reason that ‘one-off’ (type-2) alleles should be absent from the population prior to duplication.” The reason for no “one-off” alleles before duplication in our model is that intermediate mutations are assumed to be deleterious in a singlecopy gene.In the Discussion, Lynch writes, “Behe and Snoke failed to realize that a completely linked pair of duplicate genes has a mutational advantage equal to the mutation rate to null alleles. . . .” Such an effect does not hold for a model like ours in which intermediate mutations are postulated to be deleterious.A recent report (Gao and Innan 2004) presents evidence that the gene duplication rate is lower by several orders of magnitude than that assumed both by Lynch and by us based on the work of Lynch and Conery (2000). If so, then both his and our calculations for the population sizes needed to fix a mutation in a duplicated gene are substantial underestimates.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253464/

So Behe has addressed Lynchs ideas about the evolution of complexity. Maybe you weren't aware of these?

Or of course, you can keep moving the goal posts. Perhaps Behe didn't address a very specific point that Lynch raised? I'm sure you can come up with SOMETHING that Behe didn't address! :P

When you invoke evolution as the mechanism that has produced your understanding of that mechanism, your rationality is in question. Why do you suppose the non-rational process of evolution can produce a fully rational understanding of the cosmos. Evolution, if believed, has produced a near universal god-consciousness in humans. How is that rational? Yet you are claiming that the mental faculties that produce the universality of god-consciousness can be relied on to correctly perceive material phenomena and explain its origin. There is no basis for knowing that to be true.

When you invoke magic as the mechanism that has produced your understanding of that mechanism, your rationality is in question. Why do you suppose the non-rational process of magic can produce a fully rational understanding of the cosmos. Magic, if believed, has produced a near universal science-consciousness in humans. How is that rational?

Yet you are claiming that the mental faculties that produce the universality of science-consciousness can be relied on to correctly perceive supernatural phenomena and explain its origin. There is no basis for knowing that to be true.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.